true append initial commit

[stevenweaver]

To run:

hivtrace -i examples/trueAppend/Network-New-4.fas -t 0.04 -r ./test/rsrc/HXB2_1497.fasta -a skip -g 0.015 -m 500 --input-old-dists examples/trueAppend/Network-New-3.tn93.csv --input-old-fasta examples/trueAppend/Network-New-3.fas --true-append --skip-alignment